Can you pull the box out yourself?
Factor in at least $1000 if you can't, and there's probably a few "while you're there" jobs that should be done while the box is off, including the rear main seal and kidney plate, as well as considering doing the clutch.
As for rebuilding the box, hopefully someone else will weigh in there.
As a random aside, if your 6 speed is anything like my 6 speed, 5000rpm shift into 6th is how many kph exactly?